In sugar beet (Beta vulgaris), virus yellows disease (VY) is caused by a complex of different aphid-transmitted virus species, with Myzus persicae being the most important vector. In Europe, beet yellows virus, beet mild yellowing virus, beet chlorosis virus and beet mosaic virus are the main causatives and impact sugar beet cultivation not only in single but also in co- and multi-infection. Co-infection can enhance replication, tissue spread, vector transmission and other fitness components of at least one of the viruses involved and influence host range, cellular tropism and vector preference. Furthermore, multi-infection of closely related viruses is the starting point for RNA recombination initiating the formation of new, often more virulent strains. As natural multi-virus resistance cannot be expected to be available in the Beta genepool and conventional virus control by reducing vector populations through insecticide treatment was banned, alternative solutions controlling the disease are urgently required. Having this in mind, our project aims to understand viral interactions during host co-colonization as well as vector interactions that are altered by multi-infections and might acerbate impact on plants and increase transmission, respectively. On the virus-plant level, we aim to decipher putative synergistic interactions, identify by transcriptomics plant factors involved and characterize metabolic pathways that are manipulated by VY in single- compared to selected co-/multi-infections. On the level of vector manipulation by the virus infection, effects on aphid behaviour as well as virus transmission preferences in co-infections shall be characterized. The aim of this project is a better understanding of the tight interactions between the three components of the pathosystem (plant-virus-vector) in a multi-infection context, which is a biological reality. Ultimately, this project could identify targets for future safe and sustainable control measures.

Downy mildew (DM), caused by the Oomycete Plasmopara viticola, is a major grapevine disease. DM leads to an intensive use of fungicides in viticulture, which impacts environment and health. In order to reduce fungicide use, breeding programs in both Germany and France have introgressed resistance loci from wild Vitis species into cultivated grapevine, resulting in new vine cultivars resistant to DM. However, the resistance mechanisms mediated by these loci are poorly characterized. Recent resistant vine varieties combine at least two independent resistance loci to DM, in order to limit the risk of resistance breakdown, which has been observed previously. Using a combination of genetic and molecular approaches together with high precision phenotyping techniques, French and German partners will explore the functional diversity of defense mechanisms associated to DM-resistance genes, in order to optimize their combination in new grapevine varieties for improved durability of resistance.

Due to the recent pesticide ban in Europe, crops are suffering from the diseases caused by insect transmitted viruses. In particular, aphid-borne Pea Enation Mosaic Virus (PEMV) causes serious yield loss in pea (Pisum sativum), an important source of protein. Although some PEMV resistant pea genotypes were identified, resistance genes are not cloned, and the infection process and the mechanisms of symptom development are not understood at a molecular level. Recently, Partner 1 has screened a collection of 240 Pisum genotypes, conducted Genome Wide Association Study (GWAS) and identified a locus involved in quantitative resistance to the pea aphid, Acyrthosiphon pisum, a major pest of pea and the vector of PEMV. There was no strong-effect resistance gene that prevents the aphid to feed on peas, hence the aphid can inoculate the virus to all the genotypes. To identify pea genes that are involved in PEMV transmission, within-host propagation and symptom development, we propose to screen the collection of 240 pea genotypes, completed with some known PEMV resistant and susceptible genotypes, for partial or total resistance against PEMV. We will evaluate PEMV spread and symptom development after aphid inoculation and conduct several GWAS to identify pea genes involved in the resistance to different steps of the infection process. In the same time, we will evaluate the virus induced changes in pea biology using transcriptomics and also in aphid-plant interactions by monitoring aphid performances and feeding behaviour. The identified genes and pathways involved in virus infection and pea-virus-aphid interactions will be examined by functional analyses. The project will identify multiple genes that are involved in virus infection and contributes to understand the mechanisms of viral infection including transmission and its effect on plant-aphid interactions.

The general objective of the URIVir project is to understand the biological impact of RNA uridylation on the pathogenicity of phytoviruses. RNA uridylation, the 3’ tailing of RNAs with uridines, is a regulatory post-transcriptional modification, conserved across most eukaryotes. RNA uridylation plays key roles in gene expression, from promoting the maturation of major non-coding RNAs to favoring the degradation of a plethora of other ones, including small RNAs. Uridylation can also tag mRNAs to trigger both 5’-3’ and 3’-5’ degradation. In fact, the full extent of the roles played by RNA uridylation is still being explored and, of note in the context of the URIVir project, RNA uridylation is emerging as a modulator of viral infection. The uridylation of viral RNAs has been reported recently in several organisms including plants and animals. To date, mechanistic insights on the roles of RNA uridylation in host-virus interactions remain fragmentary, with a single recent study revealing a negative impact of RNA uridylation on infection of Caenorhabditis elegans by the Orsay virus and on infection of mammalian cells by the influenza virus. Importantly, detailed mechanistic information and biological insights of the roles of RNA uridylation remain unexplored for plant viruses. The URIVir project is specifically designed to address this question. In URIVir, RNA uridylation patterns for a range of model and economically relevant plant viruses will be investigated by high-throughput sequencing methods. This analysis will determine the evolutionary conservation of RNA uridylation among the major families of (+)ssRNA phytoviruses. We will identify factors involved in viral RNA uridylation and define how this RNA modification modulates the pathogenicity of selected plant viruses and participates in plant defence against viruses. URIVir will benefit from complementary expertise of two partners: Partner1 (P1) regroups experts in RNA uridylation, RNA degradation and plant virology, and Partner2 (P2) is a leading team in the study of grapevine fanleaf virus (GFLV). GFLV is the main causal agent of grapevine fanleaf degeneration disease, responsible for drastic yield losses worldwide. The URIVir project is grounded on key preliminary results jointly obtained by P1&P2. P1 has developed HTS-based tools to study the uridylation status of Arabidopsis transcripts. In a collaborative effort, P1&P2 used such tools to determine the uridylation patterns for six viruses selected from diverse families and including the nepovirus GFLV. Uridylation was detected for all viral RNAs tested, indicating that uridylation is a widespread feature of phytoviruses. Yet, uridylation levels can be extremely diverse between viruses, ranging from less than 1% to more than 90%. Uridylation can be strictly restricted to the addition of a single uridine or corresponds to short U-tails, depending on the viral RNAs. Altogether, those data suggest a complexity and diversity of molecular processes linked to the uridylation of viral RNAs. We will explore this diversity of uridylation-related processes to determine their influence on plant-virus interaction. URIVir is a basic science project, which aims at understanding fundamental regulatory processes. However, we anticipate that the combined use of model and agronomically relevant viruses will accelerate fundamental discoveries and allow a fast transfer of knowledge to agronomically relevant viruses and crop species. RNA viruses represent 80% of the plant infecting viruses and result in diseases strongly affecting agricultural yields, thereby representing a major threat to food security and economy. Deciphering the molecular bases of RNA virus multiplication and their interactions with the host cellular machinery is therefore crucial to identify novel strategies for developing innovative crop management allowing to reduce damage caused by viral diseases.

The richness of grapevine (Vitis vinifera) metabolism and its potential for giving rise to an exceptional diversity of flavor compounds contribute greatly to the aromatic complexity of wine. Indeed, analysis of the grapevine reference genome has shown a remarkable expansion of several gene families linked to secondary metabolism, compared to other plants. A striking example of gene family expansion is the terpene synthase (TPS) family that generates aromatic molecules constituting major contributors to wine flavors. Grapevine exhibits the largest TPS family of all plant species for which a genome sequence is available. Interestingly, the expansion of the TPS family in grapevine has been accompanied by a parallel blooming of some cytochrome P450 subfamilies, in particular those recently shown to be involved in the oxidation of monoterpenols. Taking advantage of the availability of several wild and cultivated Vitis genome sequences, the InteGrape project proposes to combine genomic, genetic, evolutionary and functional genomics approaches to investigate jointly the TPS and P450 genes families. This integrated approach will allow us to decipher the evolutionary mechanisms that led to the expansion of these families, to assess the impact of this expansion on the production and diversification of grape berry aroma and to evaluate the potential impact of domestication on the genes involved in grapevine aroma metabolism.